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Abstract Background Pompe Disease (PD) is a metabolic myopathy caused by variants in the GAA gene, resulting in deficient enzymatic activity. We aimed to characterize the clinical features and related genetic variants in a series of Mexican patients. Methods We performed a retrospective study of clinical records of patients diagnosed with LOPD, IOPD or pseudodeficiency. Results Twenty‐nine patients were included in the study, comprising these three forms. Overall, age of symptom onset was 0.1 to 43 years old. The most frequent variant identified was c.‐32‐13T>G, which was detected in 14 alleles. Among the 23 different variants identified in the GAA gene, 14 were classified as pathogenic, 5 were likely pathogenic, and 1 was a variant of uncertain significance. Two variants were inherited in cis arrangement and 2 were pseudodeficiency‐related benign alleles. We identified two novel variants (c.1615 G>A and c.1076‐20_1076‐4delAAGTCGGCGTTGGCCTG). Conclusion To the best of our knowledge, this series represent the largest phenotypic and genotypic characterization of patients with PD in Mexico. Patients within our series exhibited a combination of LOPD and IOPD associated variants, which may be related to genetic diversity within Mexican population. Further population‐wide studies are required to better characterize the incidence of this disease in Mexican population.